Contacts of the strand formed by residues 811 - 820 (chain K) in PDB entry 6R90
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 811 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787K GLU 5.0 1.4 - - - +
789K HIS* 3.8 17.5 + - - +
807K PHE* 4.2 5.8 - - + +
808K LEU* 3.1 37.0 + - + +
809K GLN 3.1 1.8 - - - -
810K ASN* 1.3 77.9 - - - +
812K TYR* 1.3 64.5 + - - +
833K THR* 2.5 34.7 + - + +
834K ALA 3.3 15.7 + - - +
835K MET* 3.7 25.7 - - - +
846K GLY 5.3 0.3 - - - -
847K ARG* 2.6 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 812 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722K ARG* 4.7 5.6 - - - -
787K GLU* 3.0 47.3 + - + +
789K HIS* 3.2 27.4 - + + -
810K ASN* 4.4 6.3 - - - -
811K GLU* 1.3 79.3 - - - +
813K ALA* 1.3 60.3 + - - +
814K LEU* 3.9 14.0 + - + +
833K THR* 3.2 5.2 - - - -
834K ALA* 2.9 33.1 + - + +
836K VAL* 3.8 22.4 - - + -
70L VAL* 3.3 29.8 - - + -
71L ARG* 2.7 51.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 813 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722K ARG* 4.5 9.5 + - - +
736K LEU* 3.9 24.8 - - + +
789K HIS* 3.2 23.7 + - + +
790K ASN 5.7 0.4 - - - +
807K PHE* 4.1 17.9 - - + -
811K GLU 4.0 0.8 + - - -
812K TYR* 1.3 71.9 - - - +
814K LEU* 1.3 64.6 + - - +
831K VAL* 3.9 24.0 - - + -
832K GLY 3.6 4.9 - - - -
833K THR* 4.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 814 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722K ARG* 4.8 12.1 - - - +
723K LYS* 3.8 19.1 - - - +
736K LEU* 4.0 4.3 - - - -
812K TYR* 3.9 26.7 - - + +
813K ALA* 1.3 82.6 - - - +
815K SER* 1.3 62.3 + - - +
832K GLY 2.9 7.6 + - - +
833K THR* 5.0 0.9 - - - -
834K ALA* 4.6 8.1 - - + +
869K ALA* 4.4 22.9 - - + -
870K VAL 4.1 16.2 - - - +
871K TYR* 4.5 18.8 - - + +
70L VAL* 4.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 815 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723K LYS* 4.5 6.7 - - - +
736K LEU* 3.6 8.2 - - - +
814K LEU* 1.3 78.7 - - - +
816K LEU* 1.3 61.7 + - - +
817K VAL* 6.0 0.4 - - - -
830K ILE 4.5 0.4 - - - -
831K VAL* 3.4 4.7 - - - +
832K GLY* 3.0 34.6 + - - -
870K VAL 3.2 16.8 + - - -
871K TYR 3.4 20.7 - - - -
872K SER* 4.2 8.5 + - - -
873K MET* 4.3 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 816 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723K LYS* 4.4 19.1 - - + +
724K ILE* 4.8 1.4 - - - +
725K CYS* 4.0 21.1 - - - +
734K GLY* 3.5 34.5 - - - +
735K VAL* 4.0 3.1 - - - +
736K LEU* 3.8 20.4 - - + +
791K LEU* 4.0 15.0 - - + -
815K SER* 1.3 76.9 - - - +
817K VAL* 1.3 75.9 + - - +
829K PHE* 4.4 12.8 - - + -
830K ILE 3.2 12.3 - - - +
831K VAL* 3.3 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 817 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725K CYS* 3.9 10.8 - - + -
815K SER* 6.0 0.4 - - - -
816K LEU* 1.3 83.0 - - - +
818K SER* 1.3 72.7 + - - +
819K CYS* 4.2 9.2 - - + -
828K TYR 3.8 0.2 - - - +
829K PHE* 3.5 2.1 - - - -
830K ILE* 2.7 47.5 + - + +
873K MET* 3.3 41.7 - - + +
874K VAL* 4.4 2.2 - - + +
875K GLU* 3.8 22.2 - - - +
880K LEU* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 818 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725K CYS* 3.5 24.3 - - - +
726K TYR 4.0 13.7 + - - +
727K GLN* 2.6 42.5 + - - +
817K VAL* 1.3 75.5 - - - +
819K CYS* 1.3 65.5 + - - +
827K THR* 3.6 3.5 - - - +
828K TYR 3.3 5.2 - - - -
829K PHE* 3.7 5.2 - - - -
875K GLU* 3.4 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 819 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817K VAL* 4.4 8.1 - - + -
818K SER* 1.3 77.8 + - - +
820K LYS* 1.3 59.5 - - - +
821K LEU* 3.9 19.5 + - - +
826K ASN 4.4 0.2 - - - +
827K THR* 3.4 9.6 - - - +
828K TYR* 3.1 33.5 + - - +
830K ILE* 3.6 30.5 - - - -
875K GLU* 3.3 40.4 - - + +
880K LEU* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 820 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729K VAL* 6.0 4.2 - - + +
819K CYS* 1.3 79.2 - - - +
821K LEU* 1.3 68.3 + - - +
824K ASP 3.9 3.4 - - - +
825K PRO* 2.3 49.8 + - - +
826K ASN 3.9 7.6 - - - +
827K THR* 3.4 22.7 + - + +
875K GLU* 4.4 8.6 + - - +
878K GLY* 4.7 8.4 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il